Add DB models & views for fitting specifications

weblab/accounts/managers.py

@@ -7,8 +7,7 @@ def admins(self):
 
     def create_user(self, email, full_name, institution='', password=None):
         """
-        Creates and saves a superuser with the given email, date of
-        birth and password.
+        Creates and saves a user with the given details and password.
         """
         user = self.model(
             email=self.normalize_email(email),
@@ -22,8 +21,7 @@ def create_user(self, email, full_name, institution='', password=None):
 
     def create_superuser(self, email, full_name, institution, password):
         """
-        Creates and saves a superuser with the given email, date of
-        birth and password.
+        Creates and saves a superuser with the given details and password.
         """
         user = self.create_user(
             email,

weblab/accounts/views.py

@@ -37,6 +37,7 @@ def get_success_url(self):
 
     def get_context_data(self, **kwargs):
         perms = {
+            'entities.create_fittingspec',
             'entities.create_protocol',
             'entities.create_model',
         }

weblab/config/settings/base.py

@@ -56,6 +56,7 @@
     'datasets',
     'entities',
     'experiments',
+    'fitting',
     'repocache',
 ]
 

weblab/config/urls.py

@@ -32,5 +32,6 @@
     url(r'^entities/', include('entities.urls', namespace='entities')),
     url(r'^datasets/', include('datasets.urls', namespace='datasets')),
     url(r'^experiments/', include('experiments.urls', namespace='experiments')),
+    url(r'^fitting/', include('fitting.urls', namespace='fitting')),
     url(r'^admin/', admin.site.urls),
 ]

weblab/core/context_processors.py

@@ -16,4 +16,5 @@ def common(request):
         'VISIBILITY_HELP': visibility.HELP_TEXT,
         'ERROR_MESSAGES': error_messages,
         'INFO_MESSAGES': info_messages,
+        'current_namespace': request.resolver_match.namespace,
     }

weblab/core/recipes.py

@@ -11,6 +11,11 @@
     'ProtocolEntity',
     entity_type='protocol', name=seq('myprotocol')
 )
+fittingspec = Recipe(
+    'FittingSpec',
+    entity_type='fittingspec', name=seq('myspec'),
+    protocol=foreign_key(protocol),
+)
 
 model_file = Recipe('EntityFile', entity=foreign_key(model))
 protocol_file = Recipe('EntityFile', entity=foreign_key(protocol))

weblab/entities/forms.py

@@ -15,7 +15,7 @@ def clean_name(self):
         name = self.cleaned_data['name']
         if self._meta.model.objects.filter(name=name).exists():
             raise ValidationError(
-                'You already have a %s named "%s"' % (self.entity_type, name))
+                'You already have a %s named "%s"' % (self._meta.model.display_type, name))
 
         return name
 
@@ -69,7 +69,9 @@ class EntityVersionForm(forms.Form):
     def __init__(self, *args, **kwargs):
         entity_type = kwargs.pop('entity_type')
         super().__init__(*args, **kwargs)
-        self.fields['rerun_expts'].label = self.fields['rerun_expts'].label % entity_type
+        rerun_field = self.fields.get('rerun_expts', None)
+        if rerun_field:
+            rerun_field.label = rerun_field.label % entity_type
 
 
 class EntityChangeVisibilityForm(UserKwargModelFormMixin, forms.Form):

weblab/entities/migrations/0015_auto_20191128_1601.py

@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.20 on 2019-11-28 16:01
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('entities', '0014_entity_is_fitting_spec'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='entity',
+            options={'ordering': ['name'], 'permissions': (('create_model', 'Can create models'), ('create_protocol', 'Can create protocols'), ('create_fittingspec', 'Can create fitting specifications'), ('edit_entity', 'Can edit entity'), ('moderator', 'Can promote public entity versions to moderated'))},
+        ),
+        migrations.AlterField(
+            model_name='entity',
+            name='entity_type',
+            field=models.CharField(choices=[('model', 'model'), ('protocol', 'protocol'), ('fittingspec', 'fittingspec')], max_length=16),
+        ),
+    ]

weblab/entities/models.py

@@ -19,15 +19,28 @@
 
 
 class Entity(UserCreatedModelMixin, models.Model):
+    """
+    Base class for 'entities' - conceptual entities backed by git repositories.
+
+    Subclasses describe (CellML) models, protocols, and fitting specifications.
+
+    The entity_type column states which concrete type each DB row represents, and is fixed by each subclass.
+    In addition, other class properties defined in subclasses refer to these types in helpful ways:
+    - ``other_type`` refers to the other axis on a models vs protocols matrix
+    - ``display_type`` is used to display the type of the entity to users in templates
+    - ``url_type`` is used as a URL fragment to refer to this entity type
+    """
     DEFAULT_VISIBILITY = Visibility.PRIVATE
 
     VISIBILITY_HELP = VIS_HELP_TEXT
 
     ENTITY_TYPE_MODEL = 'model'
     ENTITY_TYPE_PROTOCOL = 'protocol'
+    ENTITY_TYPE_FITTINGSPEC = 'fittingspec'
     ENTITY_TYPE_CHOICES = (
         (ENTITY_TYPE_MODEL, ENTITY_TYPE_MODEL),
         (ENTITY_TYPE_PROTOCOL, ENTITY_TYPE_PROTOCOL),
+        (ENTITY_TYPE_FITTINGSPEC, ENTITY_TYPE_FITTINGSPEC),
     )
 
     entity_type = models.CharField(
@@ -48,6 +61,7 @@ class Meta:
         permissions = (
             ('create_model', 'Can create models'),
             ('create_protocol', 'Can create protocols'),
+            ('create_fittingspec', 'Can create fitting specifications'),
             # Edit entity is used as an object-level permission
             ('edit_entity', 'Can edit entity'),
             ('moderator', 'Can promote public entity versions to moderated'),
@@ -269,18 +283,45 @@ def create(self, **kwargs):
         kwargs['entity_type'] = self.model.entity_type
         return super().create(**kwargs)
 
+    def visible_to_user(self, user):
+        """Query over all managed entities that the given user can view.
+
+        This includes those entities of the managed ``entity_type`` for which either:
+        - the user is the author
+        - the entity has at least one non-private version
+        - or the entity is explicitly shared with the user
+        """
+        from repocache.models import CACHED_VERSION_TYPE_MAP
+        CachedEntityVersion = CACHED_VERSION_TYPE_MAP[self.model.entity_type]
+        non_private = self.annotate(
+            non_private=models.Exists(
+                CachedEntityVersion.objects.filter(
+                    entity__entity=models.OuterRef('pk'),
+                    visibility__in=['public', 'moderated'],
+                )
+            )
+        ).filter(
+            non_private=True,
+        )
+        owned = self.filter(author=user)
+        shared = self.shared_with_user(user)
+        return owned | non_private | shared
+
     def shared_with_user(self, user):
         """Query over all managed entities shared explicitly with the given user."""
         if user.is_authenticated:
-            return get_objects_for_user(user, 'entities.edit_entity', with_superuser=False).filter(
-                entity_type=self.model.entity_type)
+            shared_pks = get_objects_for_user(
+                user, 'entities.edit_entity', with_superuser=False).values_list('pk', flat=True)
+            return self.get_queryset().filter(pk__in=shared_pks)
         else:
             return self.none()
 
 
 class ModelEntity(Entity):
     entity_type = Entity.ENTITY_TYPE_MODEL
     other_type = Entity.ENTITY_TYPE_PROTOCOL
+    display_type = 'model'
+    url_type = 'model'
 
     objects = EntityManager()
 
@@ -292,6 +333,8 @@ class Meta:
 class ProtocolEntity(Entity):
     entity_type = Entity.ENTITY_TYPE_PROTOCOL
     other_type = Entity.ENTITY_TYPE_MODEL
+    display_type = 'protocol'
+    url_type = 'protocol'
 
     objects = EntityManager()
 

weblab/entities/signals.py

@@ -11,4 +11,5 @@ def entity_deleted(sender, instance, **kwargs):
     """
     Signal callback when an entity is about to be deleted.
     """
-    instance.repo.delete()
+    if instance.repo_abs_path.exists():
+        instance.repo.delete()